Author: chinmoy
Date: 2009-07-24 14:20:28 -0700 (Fri, 24 Jul 2009)
New Revision: 17559
Modified:
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/cladograms/CircularCladogram.java
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/cladograms/RadialCladogram.java
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/cladograms/RectangularCladogram.java
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/phylograms/CircularPhylogram.java
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/phylograms/RectangularPhylogram.java
Log:
Modified:
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/cladograms/CircularCladogram.java
===================================================================
---
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/cladograms/CircularCladogram.java
2009-07-24 20:18:02 UTC (rev 17558)
+++
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/cladograms/CircularCladogram.java
2009-07-24 21:20:28 UTC (rev 17559)
@@ -104,6 +104,17 @@
// Find the root of the tree
Node root = commonFunctions.getTreeRoot(network);
+ // Remove bends
+
+ List<Edge> allEdges = network.edgesList();
+ Iterator<Edge> edgesIterator = allEdges.iterator();
+
+ while(edgesIterator.hasNext())
+ {
+
+ Edge edge = edgesIterator.next();
+ networkView.getEdgeView(edge).clearBends();
+ }
numLeavesVisited = 0;
// Obtain post order traversal of nodes starting from the root
@@ -128,8 +139,8 @@
// Bend each edge to make it look circular
- List<Edge> allEdges = network.edgesList();
- Iterator<Edge> edgesIterator = allEdges.iterator();
+ allEdges = network.edgesList();
+ edgesIterator = allEdges.iterator();
while(edgesIterator.hasNext())
{
Modified:
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/cladograms/RadialCladogram.java
===================================================================
---
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/cladograms/RadialCladogram.java
2009-07-24 20:18:02 UTC (rev 17558)
+++
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/cladograms/RadialCladogram.java
2009-07-24 21:20:28 UTC (rev 17559)
@@ -154,7 +154,6 @@
double nodeX = radius * Math.cos(angle);
double nodeY = radius * Math.sin(angle);
- System.out.println(node.getIdentifier()+":"+angle);
networkView.getNodeView(node).setXPosition(nodeX,true);
networkView.getNodeView(node).setYPosition(nodeY, true);
Modified:
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/cladograms/RectangularCladogram.java
===================================================================
---
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/cladograms/RectangularCladogram.java
2009-07-24 20:18:02 UTC (rev 17558)
+++
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/cladograms/RectangularCladogram.java
2009-07-24 21:20:28 UTC (rev 17559)
@@ -103,7 +103,17 @@
// Find the root of the tree
Node root = commonFunctions.getTreeRoot(network);
+ // Remove bends
+ List<Edge> allEdges = network.edgesList();
+ Iterator<Edge> edgesIterator = allEdges.iterator();
+
+ while(edgesIterator.hasNext())
+ {
+
+ Edge edge = edgesIterator.next();
+ networkView.getEdgeView(edge).clearBends();
+ }
numLeavesVisited = 0;
// Obtain post order traversal of nodes starting from the root
@@ -127,8 +137,8 @@
// Bend each edge to make it look rectangular
- List<Edge> allEdges = network.edgesList();
- Iterator<Edge> edgesIterator = allEdges.iterator();
+ allEdges = network.edgesList();
+ edgesIterator = allEdges.iterator();
while(edgesIterator.hasNext())
{
Modified:
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/phylograms/CircularPhylogram.java
===================================================================
---
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/phylograms/CircularPhylogram.java
2009-07-24 20:18:02 UTC (rev 17558)
+++
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/phylograms/CircularPhylogram.java
2009-07-24 21:20:28 UTC (rev 17559)
@@ -115,6 +115,17 @@
// Intialize the common functions
commonFunctions = new CommonFunctions();
+ // Remove bends
+
+ List<Edge> allEdges = network.edgesList();
+ Iterator<Edge> edgesIterator = allEdges.iterator();
+
+ while(edgesIterator.hasNext())
+ {
+
+ Edge edge = edgesIterator.next();
+ networkView.getEdgeView(edge).clearBends();
+ }
// Find the root of the tree
Node root = commonFunctions.getTreeRoot(network);
@@ -149,8 +160,8 @@
// Bend each edge to make it look circular
- List<Edge> allEdges = network.edgesList();
- Iterator<Edge> edgesIterator = allEdges.iterator();
+ allEdges = network.edgesList();
+ edgesIterator = allEdges.iterator();
while(edgesIterator.hasNext())
{
Modified:
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/phylograms/RectangularPhylogram.java
===================================================================
---
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/phylograms/RectangularPhylogram.java
2009-07-24 20:18:02 UTC (rev 17558)
+++
csplugins/trunk/soc/chinmoy/phylotree/src/org/cytoscape/phylotree/layout/phylograms/RectangularPhylogram.java
2009-07-24 21:20:28 UTC (rev 17559)
@@ -115,7 +115,17 @@
// Intialize the common functions
commonFunctions = new CommonFunctions();
-
+ // Remove bends
+
+ List<Edge> allEdges = network.edgesList();
+ Iterator<Edge> edgesIterator = allEdges.iterator();
+
+ while(edgesIterator.hasNext())
+ {
+
+ Edge edge = edgesIterator.next();
+ networkView.getEdgeView(edge).clearBends();
+ }
// Find the root of the tree
Node root = commonFunctions.getTreeRoot(network);
@@ -151,8 +161,8 @@
// Bend each edge to make it look rectangular
- List<Edge> allEdges = network.edgesList();
- Iterator<Edge> edgesIterator = allEdges.iterator();
+ allEdges = network.edgesList();
+ edgesIterator = allEdges.iterator();
while(edgesIterator.hasNext())
{
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